Swiss Institute of Bioinformatics (SIB) View Institution's Website 5 articles published in JoVE Cancer Research Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment Cinzia Donato*1, Barbara M. Szczerba*1, Manuel C. Scheidmann*1, Francesc Castro-Giner1,2, Nicola Aceto1 1Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 2SIB Swiss Institute of Bioinformatics Here, we present an integrated workflow to identify phenotypic and molecular features that characterize circulating tumor cells (CTCs). We combine live immunostaining and robotic micromanipulation of single and clustered CTCs with single cell-based techniques for downstream analysis and assessment of metastasis-seeding ability. Medicine An Optimized Hemagglutination Inhibition (HI) Assay to Quantify Influenza-specific Antibody Titers Lukas Kaufmann*1, Mohammedyaseen Syedbasha*1, Dominik Vogt1, Yvonne Hollenstein1, Julia Hartmann1, Janina E. Linnik1,2,3, Adrian Egli1,4 1Applied Microbiology Research, Department of Biomedicine, University of Basel, 2Department of Biosystems Science and Engineering, ETH Zurich, 3Swiss Institute of Bioinformatics, 4Clinical Microbiology, University Hospital Basel The presented protocols describe how to perform a hemagglutination inhibition assay to quantify influenza-specific antibody titers from serum samples of influenza vaccine recipients. The first assay determines optimal viral antigen concentrations by hemagglutination. The second assay quantifies influenza-specific antibody titers by hemagglutination inhibition. Chemistry An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions Mohameedyaseen Syedbasha1, Janina Linnik1,2,3, Deanna Santer4, Daire O'Shea5, Khaled Barakat4,6, Michael Joyce4, Nina Khanna7, D. Lorne Tyrrell4, Michael Houghton4, Adrian Egli1,8 1Applied Microbiology Research, Department of Biomedicine, University of Basel, 2Department of Biosystems Science and Engineering, ETH Zurich, and Swiss Institute of Bioinformatics, 3Swiss Institute of Bioinformatics, 4Li Ka Shing Institute for Virology, University of Alberta, 5Regional Infectious Diseases Unit, University of Edinburgh, 6Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, 7Infection Biology, Department of Biomedicine, University of Basel, 8Clinical Microbiology, University Hospital Basel The presented protocols describe two enzyme-linked immunosorbent assay (ELISA) based techniques for the rapid investigation of ligand-receptor interactions: The first assay allows the determination of dissociation constant between ligand and receptor. The second assay enables a rapid screening of blocking peptides for ligand-receptor interactions. Environment Physical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells Tina Wunderlin1, Thomas Junier2, Christophe Paul3, Nicole Jeanneret3, Pilar Junier3 1Department of Biological Sciences, Macquarie University, 2Vital-IT group, Swiss Institute of Bioinformatics, 3Laboratory of Microbiology, University of Neuchatel A method to single out bacterial endospores from complex microbial communities was developed to perform tailored culture or molecular studies of this group of bacteria. Medicine Improved Protocol For Laser Microdissection Of Human Pancreatic Islets From Surgical Specimens Dorothée Sturm1,2, Lorella Marselli3, Florian Ehehalt1,2, Daniela Richter1, Marius Distler2, Stephan Kersting1,2, Robert Grützmann2, Krister Bokvist4, Philippe Froguel5, Robin Liechti6, Anne Jörns7, Paolo Meda8, Gustavo Bruno Baretton9, Hans-Detlev Saeger2, Anke M. Schulte10, Piero Marchetti3, Michele Solimena1 1Molecular Diabetology, Paul Langerhans Institute Dresden, 2Department of GI-, Thoracic- and Vascular Surgery, University Hospital Carl Gustav Carus, University of Technology Dresden, 3Department of Endocrinology and Metabolism, Metabolic Unit University of Pisa, 4Labs DC0522, Lilly Corporate Center, 5Genomics, Faculty of Medicine Imperial College London, 6Vital-IT, SIB Swiss Institute of Bioinformatics, 7Clinical Biochemistry, Hannover Medical School, 8Cell Physiology and Metabolism, Medical School, University of Geneva, 9Department of Pathology, University Hospital Carl Gustav Carus, University of Technology Dresden, 10R&D DIAB Division / Translational Medicine, Sanofi-Aventis Laser microdissection is a technique that allows the recovery of selected cells from minute amounts of parenchyma. Here we describe a protocol for acquiring human pancreatic islets from surgical specimens to be used for transcriptomic studies. Our protocol improves the intrinsic autofluorescence of human beta cells, thus facilitating their collection.